Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple

Proof of concept of Bayesian integrated QTL analyses across pedigree-related families from breeding programs of an outbreeding species. Results include QTL confidence intervals, individuals' genotype probabilities and genomic breeding values. Bayesian QTL linkage mapping approaches offer the flexibility to study multiple full sib families with known pedigrees simultaneously. Such a joint analysis increases the probability of detecting these quantitative trait loci (QTL) and provide insight of the magnitude of QTL across different genetic backgrounds. Here, we present an improved Bayesian multi-QTL pedigree-based approach on an outcrossing species using progenies with different (complex) genetic relationships. Different modeling assumptions were studied in the QTL analyses, i.e., the a priori expected number of QTL varied and polygenic effects were considered. The inferences include number of QTL, additive QTL effect sizes and supporting credible intervals, posterior probabilities of QTL genotypes for all individuals in the dataset, and QTL-based as well as genome-wide breeding values. All these features have been implemented in the FlexQTL(™) software. We analyzed fruit firmness in a large apple dataset that comprised 1,347 individuals forming 27 full sib families and their known ancestral pedigrees, with genotypes for 87 SSR markers on 17 chromosomes. We report strong or positive evidence for 14 QTL for fruit firmness on eight chromosomes, validating our approach as several of these QTL were reported previously, though dispersed over a series of studies based on single mapping populations. Interpretation of linked QTL was possible via individuals' QTL genotypes. The correlation between the genomic breeding values and phenotypes was on average 90 %, but varied with the number of detected QTL in a family. The detailed posterior knowledge on QTL of potential parents is critical for the efficiency of marker-assisted breeding.

Mapping of an anthocyanin-regulating MYB transcription factor and its expression in red and green pear, Pyrus communis

'Max Red Bartlett' is a red bud mutation of the yellow pear (Pyrus communis L.) cultivar 'Williams' (known as 'Bartlett' in North America). Anthocyanins are the most important pigments for red colour in fruits. Synthesis of anthocyanins is mediated by a number of well-characterized enzymes that include chalcone synthase (CHS), flavanone-3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-glucose:flavonoid-3-O-glucosyltransferase (UFGT). Expression of the genes encoding these five enzymes was examined in pear fruit skin in order to elucidate the molecular mechanism for red coloration. In addition, the gene PcMYB10, encoding an R2R3 MYB transcription factor involved in anthocyanin biosynthetic pathway regulation, was isolated from both 'Williams' and 'Max Red Bartlett'. Analysis of the deduced amino acid sequence suggests that this gene is an ortholog of anthocyanin regulators known in other plant species. Its expression level was significantly higher in 'Max Red Bartlett' (red pear) compared with the original yellow variety 'Williams'. Although the map position of PcMYB10 corresponds to that of MdMYBa and MdMYB10, which control pigmentation of apple fruit skin, PcMYB10 is not directly responsible for red versus yellow colour in the two pear varieties, as the mutation underlying this difference maps to a different region of the pear genome.

Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening

BACKGROUND

Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-methylcyclopropene.

RESULTS

To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated.The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening.

CONCLUSION

Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species.

QTL dynamics for fruit firmness and softening around an ethylene-dependent polygalacturonase gene in apple (Malus x domestica Borkh.)

Apple fruit are well known for their storage life, although a wide range of flesh softening occurs among cultivars. Loss of firmness is genetically coordinated by the action of several cell wall enzymes, including polygalacturonase (PG) which depolymerizes cell wall pectin. By the analysis of 'Fuji' (Fj) and 'Mondial Gala' (MG), two apple cultivars characterized by a distinctive ripening behaviour, the involvement of Md-PG1 in the fruit softening process was confirmed to be ethylene dependent by its transcript being down-regulated by 1-methylcyclopropene treatment in MG and in the low ethylene-producing cultivar Fj. Comparing the PG sequence of MG and Fj, a single nucleotide polymorphism (SNP) was discovered. Segregation of the Md-PG1(SNP) marker within a full-sib population, obtained by crossing Fj and MG, positioned Md-PG1 in the linkage group 10 of MG, co-located with a quantitative trait locus (QTL) identified for fruit firmness in post-harvest ripening. Fruit firmness and softening analysed in different stages, from harvest to post-storage, determined a shift of the QTL from the top of this linkage group to the bottom, where Md-ACO1, a gene involved in ethylene biosynthesis in apple, is mapped. This PG-ethylene-related gene has beeen positioned in the apple genome on chromosome 10, which contains several QTLs controlling fruit firmness and softening, and the interplay among the allelotypes of the linked loci should be considered in the design of a marker-assisted selection breeding scheme for apple texture.

Oxidative stress and senescence-like status of pear calli co-cultured on suspensions of incompatible quince microcalli

This work presents a simple in vitro system to study physiological, biochemical and molecular changes occurring in a pear callus (Pyrus communis L., cv. Beurré Bosc) grown in close proximity to spatially separated undifferentiated homologous (pear) or heterologous (quince; Cydonia oblonga Mill., East Malling clone C) cells in its neighboring environment. After a 7-day co-culture period, the presence of heterologous cells produced negative effects on the pear callus, whose relative weight increase and adenylate energy charge decreased by 30 and 24%, respectively. Such behavior was associated with a higher O(2) consumption rate (+125%) which did not seem to be coupled to adenosine triphosphate synthesis. Analyses of alternative oxidase and enzymatic activities involved in reactive oxygen species (ROS) detoxification strongly suggested that the higher O(2) consumption rate, measured in the pear callus grown in the heterologous combination, may probably be ascribed to extra-respiratory activities. These, in turn, might contribute to generate metabolic scenarios where ROS-induced oxidative stresses may have the upper hand. The increase in the levels of 2-thiobarbituric acid reactive metabolites, considered as diagnostic indicators of ROS-induced lipid peroxidation, seemed to confirm this hypothesis. Moreover, reverse transcription polymerase chain reaction analysis revealed that the expression levels of a few senescence-associated genes were higher in the pear callus grown in the heterologous combination than in the homologous one. Taken as a whole, physiological and molecular data strongly suggest that undifferentiated cells belonging to a pear graft-incompatible quince clone may induce an early senescence-like status in a closely co-cultured pear callus.

Mapping of the apple scab-resistance gene Vb

Apple scab, caused by the fungus Venturia inaequalis, is the major production constraint in temperate zones with humid springs. Normally, its control relies on frequent and regular fungicide applications. Because this control strategy has come under increasing criticism, major efforts are being directed toward the breeding of scab-resistant apple cultivars. Modern apple breeding programs include the use of molecular markers, making it possible to combine several different scab-resistance genes in 1 apple cultivar (pyramiding) and to speed up the breeding process. The apple scab-resistance gene Vb is derived from the Siberian crab apple 'Hansen's baccata #2', and is 1 of the 6 "historical" major apple scab-resistance genes (Vf, Va, Vr, Vbj, Vm, and Vb). Molecular markers have been published for all these genes, except Vr. In testcross experiments conducted in the 1960s, it was reported that Vb segregated independently from 3 other major resistance genes, including Vf. Recently, however, Vb and Vf have both been mapped on linkage group 1, a result that contrasts with the findings from former testcross experiments. In this study, simple sequence repeat (SSR) markers were used to identify the precise position of Vb in a cross of 'Golden Delicious' (vbvb) and 'Hansen's baccata #2' (Vbvb). A genome scanning approach, a fast method already used to map apple scab-resistance genes Vr2 and Vm, was used, and the Vb locus was identified on linkage group 12, between the SSR markers Hi02d05 and Hi07f01. This finding confirms the independent segregation of Vb from Vf. With the identification of SSR markers linked to Vb, another major apple scab-resistance gene has become available; breeders can use it to develop durable resistant cultivars with several different resistance genes.

Retrotransposon characterisation and fingerprinting of apple clones by S-SAP markers

Retrotransposons have been found to comprise the most common class of transposable elements in eukaryotes and to occur in high copy number in plant genomes. Several of these elements have been sequenced and were found to display a high degree of heterogeneity and insertional polymorphism, both within and between species. The dispersion, ubiquity and prevalence of retrotransposons in plant genomes provide an excellent basis for the development of marker systems and, hence, may be good molecular candidates in distinguishing among apple clones, when they represent bud mutations of the original variety, considering that the random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) used thus far in fingerprinting analyses have failed to meet discrimination expectations. The technique called sequence-specific amplified polymorphism (S-SAP), which makes it possible to identify dominant markers for the detection of variation in the DNA flanking the retrotransposon insertion site, was used in the present study to distinguish several clones of the cultivars 'Gala' and 'Braeburn' in apple fingerprinting. Moreover, our results suggest that the bud mutations, which have generated new patented varieties of 'Gala' and 'Braeburn', appear to derive from retrotransposon insertion.

Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm

For all known major apple scab resistance genes except Vr, molecular markers have been published. However, the precise position of some of these genes, in the apple genome, remains to be identified. Knowledge about the relative position of apple scab resistance genes is necessary to preliminarily evaluate the probability of success of their pyramidization. Pyramidization of different resistance genes into the same genotype is a reliable way to create cultivars with durable apple scab resistance. Applying the genome scanning approach (GSA), we identified the linkage group of the scab resistance gene Vm, derived from Malus micromalus, and we found a new molecular marker tightly associated with the gene. The simple sequence repeat Hi07h02, previously mapped on linkage group 17, cosegregates with the Vm gene (no recombinants in the 95 plants tested). The already published sequence-characterized amplified region Vm marker OPB12(687) was found to be linked at about 5 cM from the resistance gene and, therefore, this marker also maps on linkage group 17 of apple. This is the first report of the discovery of a major apple scab resistance gene on linkage group 17. The advantages of using GSA for the identification of molecular markers for qualitative traits are discussed.

Identification of functional apple scab resistance gene promoters

Apple scab (Venturia inaequalis) is one of the most damaging diseases affecting commercial apple production. Some wild Malus species possess resistance against apple scab. One gene, HcrVf2, from a cluster of three genes derived from the wild apple Malus floribunda clone 821, has recently been shown to confer resistance to apple scab when transferred into a scab-susceptible apple variety. For this proof-of-function experiment, the use of the 35S promoter from Cauliflower mosaic virus was reliable and appropriate. However, in order to reduce the amount of non-plant DNA in genetically modified apple to a minimum, with the aim of increasing genetically modified organism acceptability, these genes would ideally be regulated by their own promoters. In this study, sequences from the promoter region of the three members of the HcrVf gene family were compared. Promoter constructs containing progressive 5' deletions were prepared and used for functional analyses. Qualitative assessment confirmed promoter activity in apple. Quantitative promoter comparison was carried out in tobacco (Nicotiana glutinosa) and led to the identification of several promoter regions with different strengths from a basal level to half the strength of the 35S promoter from Cauliflower mosaic virus.

Characterisation and transferability of apple SSRs to two European pear F1 populations

European pear (Pyrus communis L.) is among the important fruit species for which only few genetic studies have been carried out. Available evidence indicates that simple sequence repeats (SSR) are very useful as molecular markers because they are codominant, highly polymorphic, abundant and reproducible. The present paper reports more than 100 apple SSR markers in two populations of European pear; a total of 41 SSR markers were then positioned on a genetic linkage map of the cross 'Passe Crassane' x 'Harrow Sweet' and 31 in the map 'Abbe Fetel' x 'Max Red Bartlett'. Syntenic relationships between pear and apple maps have been considered for the chromosomes carrying two or more SSR markers. The alignment among the two maps supports the colinearity of the two genomes with respect both to identification and to orientation of the linkage groups.

The HcrVf2 gene from a wild apple confers scab resistance to a transgenic cultivated variety

The Vf gene from the wild species Malus floribunda 821 is the most studied apple scab resistance gene. Several molecular markers mapping around this gene were the starting point for a positional cloning project. The analysis of the bacterial artificial chromosome clones spanning the Vf region led to the identification of a cluster of genes homologous to the Cladosporium fulvum resistance gene family of tomato. One of these genes, HcrVf2 (homologue of the C. fulvum resistance genes of the Vf region), was used to transform the susceptible apple cultivar Gala. Four independent transformed lines resistant to apple scab were produced, proving that HcrVf2 is sufficient to confer scab resistance to a susceptible cultivar. The results show that direct gene transfer between cross-compatible species can be viable when, as in apple, the use of backcrosses to introduce resistance genes from wild species cannot exactly reconstitute the heterozygous genotype of clonally propagated cultivars.

Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes cosegregating with Vf apple scab resistance

Scab caused by the fungal pathogen Venturia inaequalis is the most common disease of cultivated apple (Malus x domestica Borkh.). Monogenic resistance against scab is found in some small-fruited wild Malus species and has been used in apple breeding for scab resistance. Vf resistance of Malus floribunda 821 is the most widely used scab resistance source. Because breeding a high-quality cultivar in perennial fruit trees takes dozens of years, cloning disease resistance genes and using them in the transformation of high-quality apple varieties would be advantageous. We report the identification of a cluster of receptor-like genes with homology to the Cladosporium fulvum (Cf) resistance gene family of tomato on bacterial artificial chromosome clones derived from the Vf scab resistance locus. Three members of the cluster were sequenced completely. Similar to the Cf gene family of tomato, the deduced amino acid sequences coded by these genes contain an extracellular leucine-rich repeat domain and a transmembrane domain. The transcription of three members of the cluster was determined by reverse transcriptionpolymerase chain reaction to be constitutive, and the transcription and translation start of one member was verified by 5' rapid amplification of cDNA ends. We discuss the parallels between Cf resistance of tomato and Vf resistance of apple and the possibility that one of the members of the gene cluster is the Vf gene. Cf homologs from other regions of the apple genome also were identified and are likely to present other scab resistance genes.

Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars

We isolated and sequenced 26 microsatellites from two genomic libraries of peach cultivar 'Redhaven', enriched for AC/GT and AG/CT repeats, respectively. For 17 of these microsatellites, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was assayed in 50 peach and nectarine cultivars. Of the 1300 PCRs carried out, all but two produced amplified products of the expected size. All microsatellites were polymorphic, showing 2-8 alleles per locus. Heterozygosity ranged from 0.04-0.74 (mean 0.47); the discrimination power (PD) ranged from 0.04-0.84 (mean 0.60). Cultivar heterozygosity varied greatly, with one cultivar ('Independence') being homozygous at all loci. The set of microsatellites discriminated all cultivars investigated, except several sport mutations, i.e., 'Dixitime' vs. 'Springcrest', 'Compact Redhaven' vs. 'Redhaven', and two pairs of cultivars, 'Venus' vs. 'Orion' and 'Elegant Lady' vs. 'Rome Star', whose pedigrees are controversial. We were able to analyze the paternity of several cultivars. In most cases, the parenthood was confirmed. The comparison of three long-living 'Redhaven' accessions supplied by different repositories did not provide any evidence of somatic instability of microsatellites. Hence, microsatellites, ranked according to their information content, are recommended as markers of choice for peach fingerprinting and suggestions are provided for interpreting band profiles and the correct sizing of alleles.

Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars

We isolated and sequenced 26 microsatellites from two genomic libraries of peach cultivar 'Redhaven', enriched for AC/GT and AG/CT repeats, respectively. For 17 of these microsatellites, it was possible to demonstrate Mendelian inheritance. Microsatellite polymorphism was assayed in 50 peach and nectarine cultivars. Of the 1300 PCRs carried out, all but two produced amplified products of the expected size. All microsatellites were polymorphic, showing 2-8 alleles per locus. Heterozygosity ranged from 0.04-0.74 (mean 0.47); the discrimination power (PD) ranged from 0.04-0.84 (mean 0.60). Cultivar heterozygosity varied greatly, with one cultivar ('Independence') being homozygous at all loci. The set of microsatellites discriminated all cultivars investigated, except several sport mutations, i.e., 'Dixitime' vs. 'Springcrest', 'Compact Redhaven' vs. 'Redhaven', and two pairs of cultivars, 'Venus' vs. 'Orion' and 'Elegant Lady' vs. 'Rome Star', whose pedigrees are controversial. We were able to analyze the paternity of several cultivars. In most cases, the parenthood was confirmed. The comparison of three long-living 'Redhaven' accessions supplied by different repositories did not provide any evidence of somatic instability of microsatellites. Hence, microsatellites, ranked according to their information content, are recommended as markers of choice for peach fingerprinting and suggestions are provided for interpreting band profiles and the correct sizing of alleles.Key words: genetics, molecular markers, paternity analysis, pedigree analysis, simple sequence repeat.

Construction of a 550 kb BAC contig spanning the genomic region containing the apple scab resistance gene Vf

A positional cloning project was started in apple with the aim of isolating the Vf resistance gene of Malus floribunda 821. Vf confers resistance against apple scab, the most important disease in apple orchards. A chromosome walk starting from two molecular markers (M18-CAPS and AM19-SCAR) flanking Vf was performed, using a bacterial artificial chromosome (BAC) library containing inserts of the cultivar Florina, which is heterozygous for Vf. Thirteen BAC clones spanning the region between the two markers were identified in nine chromosome walking steps. The size of the resulting contig is approximately 550 kb. In order to map the Vf region in more detail, we analyzed over 2000 plants from different populations segregating for Vf with markers produced from BAC end sequences. In this way, we were able to restrict the possible location of the Vf gene to a minimum of five clones spanning an interval of approximately 350 kb.